int ComputeCoheLocal::compute_pairs(int flag)
{
int i,j,m,n,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,del,delx,dely,delz;
double r,rinv,radi,radj,radsum;
double ccel,ccelx,ccely,ccelz;
double rsq,eng,fpair,factor_coul,factor_lj;
int *ilist,*jlist,*numneigh,**firstneigh;
double *ptr;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
double *radius = atom->radius;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
// invoke half neighbor list (will copy or build if necessary)
if (flag == 0) neighbor->build_one(list->index);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
// skip if I or J are not in group
// for flag = 0, just count pair interactions within force cutoff
// for flag = 1, calculate requested output fields
Pair *pair = force->pair;
double **cutsq = force->pair->cutsq;
tagint *tag = atom->tag;
m = 0;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (!(mask[i] & groupbit)) continue;
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
radi = radius[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
if (!(mask[j] & groupbit)) continue;
if (newton_pair == 0 && j >= nlocal) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
radj = radius[j];
radsum = radi + radj;
// if (rsq >= cutsq[itype][jtype]) continue;
if (rsq < (radsum + smax)*(radsum + smax)){
r = sqrt(rsq);
del = r - radsum;
if (del > smin)
ccel = - ah*pow(radsum,6)/6.0/del/del/(r + radsum)/(r + radsum)
/r/r/r;
else
ccel = - ah*pow(radsum,6)/6.0/smin/smin/(smin+ 2.0*radsum)/(smin + 2.0*radsum)
/(smin + radsum)/(smin + radsum)/(smin + radsum);
rinv = 1.0/r;
ccelx = delx*ccel*rinv;
ccely = dely*ccel*rinv;
ccelz = delz*ccel*rinv;
}
else {
ccelx = 0;
ccely = 0;
ccelz = 0;
}
if (flag) {
if (singleflag)
eng = pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
if (nvalues == 1) ptr = &vector[m];
else ptr = array[m];
for (n = 0; n < nvalues; n++) {
switch (pstyle[n]) {
case DIST:
ptr[n] = sqrt(rsq);
break;
case ENG:
ptr[n] = eng;
break;
case FORCE:
ptr[n] = sqrt(rsq)*fpair;
break;
case FX:
ptr[n] = ccelx;
break;
case FY:
ptr[n] = ccely;
break;
case FZ:
ptr[n] = ccelz;
break;
case PN:
ptr[n] = pair->svector[pindex[n]];
break;
case TAG1:
ptr[n] = tag[i];
break;
case TAG2:
ptr[n] = tag[j];
break;
}
}
}
m++;
}
}
return m;
}
int ComputePairLocal::compute_pairs(int flag)
{
int i,j,m,n,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,eng,fpair,factor_coul,factor_lj;
int *ilist,*jlist,*numneigh,**firstneigh;
double *dbuf,*ebuf,*fbuf;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
// invoke half neighbor list (will copy or build if necessary)
if (flag == 0) neighbor->build_one(list->index);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
// skip if I or J are not in group
if (flag) {
if (nvalues == 1) {
if (dflag >= 0) dbuf = vector;
if (eflag >= 0) ebuf = vector;
if (fflag >= 0) fbuf = vector;
} else {
if (dflag >= 0) dbuf = &array[0][dflag];
if (eflag >= 0) ebuf = &array[0][eflag];
if (fflag >= 0) fbuf = &array[0][fflag];
}
}
Pair *pair = force->pair;
double **cutsq = force->pair->cutsq;
m = n = 0;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (!(mask[i] & groupbit)) continue;
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
if (!(mask[j] & groupbit)) continue;
if (newton_pair == 0 && j >= nlocal) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq >= cutsq[itype][jtype]) continue;
if (flag) {
if (dflag >= 0) dbuf[n] = sqrt(rsq);
if (eflag >= 0 || fflag >= 0) {
eng = pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
if (eflag >= 0) ebuf[n] = eng;
if (fflag >= 0) fbuf[n] = sqrt(rsq)*fpair;
}
n += nvalues;
}
m++;
}
}
return m;
}
int ComputePairLocal::compute_pairs(int flag)
{
int i,j,m,n,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,eng,fpair,factor_coul,factor_lj;
int *ilist,*jlist,*numneigh,**firstneigh;
double *ptr;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
// invoke half neighbor list (will copy or build if necessary)
if (flag == 0) neighbor->build_one(list->index);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
// skip if I or J are not in group
// for flag = 0, just count pair interactions within force cutoff
// for flag = 1, calculate requested output fields
Pair *pair = force->pair;
double **cutsq = force->pair->cutsq;
m = 0;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (!(mask[i] & groupbit)) continue;
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
if (!(mask[j] & groupbit)) continue;
if (newton_pair == 0 && j >= nlocal) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq >= cutsq[itype][jtype]) continue;
if (flag) {
if (singleflag)
eng = pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
if (nvalues == 1) ptr = &vector[m];
else ptr = array[m];
for (n = 0; n < nvalues; n++) {
switch (pstyle[n]) {
case DIST:
ptr[n] = sqrt(rsq);
break;
case ENG:
ptr[n] = eng;
break;
case FORCE:
ptr[n] = sqrt(rsq)*fpair;
break;
case FX:
ptr[n] = delx*fpair;
break;
case FY:
ptr[n] = dely*fpair;
break;
case FZ:
ptr[n] = delz*fpair;
break;
case PN:
ptr[n] = pair->svector[pindex[n]];
break;
}
}
}
m++;
}
}
return m;
}
int ComputePairLocal::compute_pairs(int flag)
{
int i,j,m,n,ii,jj,inum,jnum,itype,jtype;
tagint itag,jtag;
double xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,radsum,eng,fpair,factor_coul,factor_lj;
int *ilist,*jlist,*numneigh,**firstneigh;
double *ptr;
double **x = atom->x;
double *radius = atom->radius;
tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
// invoke half neighbor list (will copy or build if necessary)
if (flag == 0) neighbor->build_one(list);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
// skip if I or J are not in group
// for newton = 0 and J = ghost atom,
// need to insure I,J pair is only output by one proc
// use same itag,jtag logic as in Neighbor::neigh_half_nsq()
// for flag = 0, just count pair interactions within force cutoff
// for flag = 1, calculate requested output fields
Pair *pair = force->pair;
double **cutsq = force->pair->cutsq;
m = 0;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (!(mask[i] & groupbit)) continue;
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itag = tag[i];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
if (!(mask[j] & groupbit)) continue;
// itag = jtag is possible for long cutoffs that include images of self
if (newton_pair == 0 && j >= nlocal) {
jtag = tag[j];
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) continue;
} else {
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) {
if (x[j][1] < ytmp) continue;
if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
}
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (cutstyle == TYPE) {
if (rsq >= cutsq[itype][jtype]) continue;
} else {
radsum = radius[i] + radius[j];
if (rsq >= radsum*radsum) continue;
}
if (flag) {
if (singleflag)
eng = pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
else eng = fpair = 0.0;
if (nvalues == 1) ptr = &vlocal[m];
else ptr = alocal[m];
for (n = 0; n < nvalues; n++) {
switch (pstyle[n]) {
case DIST:
ptr[n] = sqrt(rsq);
break;
case ENG:
ptr[n] = eng;
break;
case FORCE:
ptr[n] = sqrt(rsq)*fpair;
break;
case FX:
ptr[n] = delx*fpair;
break;
case FY:
ptr[n] = dely*fpair;
break;
case FZ:
ptr[n] = delz*fpair;
break;
case PN:
ptr[n] = pair->svector[pindex[n]];
break;
}
}
}
m++;
}
}
return m;
}
